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- PDB-4nox: Structure of the nine-bladed beta-propeller of eIF3b -

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Basic information

Entry
Database: PDB / ID: 4nox
TitleStructure of the nine-bladed beta-propeller of eIF3b
ComponentsEukaryotic translation initiation factor 3 subunit B
KeywordsTRANSLATION / Beta propeller
Function / homology
Function and homology information


eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / translation initiation factor binding / translation initiation factor activity / RNA binding
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit B
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / molecular replacement / Resolution: 2.722 Å
AuthorsLiu, Y. / Neumann, P. / Kuhle, B. / Monecke, T. / Ficner, R.
CitationJournal: Structure / Year: 2014
Title: Translation initiation factor eIF3b contains a nine-bladed beta-propeller and interacts with the 40S ribosomal subunit
Authors: Liu, Y. / Neumann, P. / Kuhle, B. / Monecke, T. / Schell, S. / Chari, A. / Ficner, R.
History
DepositionNov 20, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Structure summary
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 3 subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5045
Polymers86,3631
Non-polymers1424
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.380, 108.380, 172.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-907-

HOH

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Components

#1: Protein Eukaryotic translation initiation factor 3 subunit B / eIF3b / Eukaryotic translation initiation factor 3 90 kDa subunit homolog / Translation initiation ...eIF3b / Eukaryotic translation initiation factor 3 90 kDa subunit homolog / Translation initiation factor eIF3 / p90 subunit homolog


Mass: 86362.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: PRT1, CTHT_0000230 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0RXS6
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.98 %

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPETRA III, EMBL c/o DESY P13 (MX1)10.82658
SYNCHROTRONBESSY 14.120.97981, 0.97993, 0.97749
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELApr 8, 2013
DECTRIS PILATUS 6M2PIXELMay 5, 2013
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.826581
20.979811
30.979931
40.977491
ReflectionResolution: 2.72→48.469 Å / Num. obs: 28259 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 66.87 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 25.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.72-2.820.920.6153.4824198282828280.653100
2.82-2.920.970.41520868247424720.43799.9
2.92-3.120.9820.2837.5436651402540250.3100
3.12-3.740.9970.10417.8566995777477730.11100
3.74-4.050.9990.05631.4720382229922980.059100
4.05-4.360.9990.04139.4514533169716970.043100
4.36-4.6710.03246.4810136129412940.034100
4.67-1410.02756.0745737561656100.02999.9
14-1710.01587.68001121120.017100
17-500.9980.01969.938081551500.02296.8
5012

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å46.66 Å
Translation2.8 Å46.66 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.722→48.469 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8007 / SU ML: 0.36 / σ(F): 1.36 / Phase error: 25.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2298 1412 5.01 %
Rwork0.2056 --
obs0.2069 28184 99.91 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 205.02 Å2 / Biso mean: 74.7729 Å2 / Biso min: 25.97 Å2
Refinement stepCycle: LAST / Resolution: 2.722→48.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3759 0 4 51 3814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033881
X-RAY DIFFRACTIONf_angle_d0.8065281
X-RAY DIFFRACTIONf_chiral_restr0.057553
X-RAY DIFFRACTIONf_plane_restr0.003677
X-RAY DIFFRACTIONf_dihedral_angle_d13.671409
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.722-2.81930.35881380.312626132751
2.8193-2.93220.29831390.284626232762
2.9322-3.06560.32621390.293726352774
3.0656-3.22720.33731380.258326302768
3.2272-3.42930.25291400.235826422782
3.4293-3.6940.23271380.208926542792
3.694-4.06560.23351420.196526732815
4.0656-4.65350.17521410.157526982839
4.6535-5.86130.1831430.162827222865
5.8613-48.47670.22691540.212428823036
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2455-0.226-0.0930.67470.17490.0785-0.2692-0.97520.07150.67210.44550.0665-0.46580.14120.61060.50520.0794-0.04781.38810.12110.42135.6122132.465446.361
20.1666-0.27750.10250.2442-0.13150.082-0.2085-0.80660.00440.26530.25410.28360.0502-0.33650.010.37850.13560.02840.86770.02270.3836119.0247136.818342.5193
30.10310.0758-0.02470.06920.07670.0639-0.3299-0.7110.13070.33280.2263-0.1749-0.2866-0.3109-0.00280.46890.17520.05040.8676-0.03790.3853107.2599139.996340.1389
40.4861-0.29470.22120.1147-0.13320.6803-0.1003-0.4316-0.26560.43980.17450.40820.0275-0.48550.08350.33530.00180.07890.60650.05910.4883112.3755138.176224.4919
50.252-0.1815-0.14620.1422-0.08390.31840.04340.20020.0436-0.21380.1648-0.1872-0.4472-0.4220.00270.2552-0.04920.02670.46520.02060.4264117.1765137.806711.8459
60.3471-0.3518-0.08630.37040.13960.51060.0312-0.0683-0.1676-0.15770.00990.194-0.0114-0.1617-0.00110.2135-0.0849-0.03460.30710.07210.3836127.7458123.297210.9858
70.6608-0.34570.08690.3098-0.02120.33610.0222-0.2627-0.083-0.0308-0.0812-0.0490.08720.4895-00.25930.0013-0.01580.44810.11340.3493143.0205122.525920.1277
80.2172-0.00830.0590.12150.17230.0818-0.3397-0.9458-0.20040.22920.40530.15850.17020.37310.00210.46110.11330.01291.08840.23080.5011138.8525123.485540.1206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESSEQ 166:212 )A166 - 212
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESSEQ 213:260 )A213 - 260
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESSEQ 261:293 )A261 - 293
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESSEQ 294:348 )A294 - 348
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESSEQ 349:401 )A349 - 401
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESSEQ 402:495 )A402 - 495
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESSEQ 496:592 )A496 - 592
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESSEQ 593:638 )A593 - 638

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